library("reactable")
library("htmltools")
source(here("R", "plotting.R"))
source(here("R", "tables.R"))
labels <- drake::readd("labels")
metrics <- drake::readd("metrics") %>%
filter(dataset == params$dataset)
Overall
Plot
plot_dataset_overall(metrics)

Table
make_dataset_table(metrics, labels)
Individual metrics
Overall
metric_barplot(metrics, overall, "Overall score")

Batch correction
src_list <- lapply(names(labels$metrics$batch), function(label) {
metric <- labels$metrics$batch[label]
src <- c(
"### <<label>> {.unnumbered}",
"```{r metrics-batch-<<metric>>}",
"metric_barplot(metrics, <<metric>>, '<<label>>')",
"```",
""
)
knitr::knit_expand(text = src, delim = c("<<", ">>"))
})
out <- knitr::knit_child(text = unlist(src_list), options = list(cache = FALSE))
Batch correction
metric_barplot(metrics, batch_correction, 'Batch correction')

PCR batch
metric_barplot(metrics, PCR_batch, 'PCR batch')

Batch ASW
metric_barplot(metrics, ASW_label_batch, 'Batch ASW')

Graph iLISI
metric_barplot(metrics, iLISI, 'Graph iLISI')

Graph connectivity
metric_barplot(metrics, graph_connectivity, 'Graph connectivity')

kBET
metric_barplot(metrics, kBET, 'kBET')

Bio conservation
src_list <- lapply(names(labels$metrics$bio), function(label) {
metric <- labels$metrics$bio[label]
src <- c(
"### <<label>> {.unnumbered}",
"```{r metrics-bio-<<metric>>}",
"metric_barplot(metrics, <<metric>>, '<<label>>')",
"```",
""
)
knitr::knit_expand(text = src, delim = c("<<", ">>"))
})
out <- knitr::knit_child(text = unlist(src_list), options = list(cache = FALSE))
Bio conservation
metric_barplot(metrics, bio_conservation, 'Bio conservation')

NMI cluster/label
metric_barplot(metrics, NMI_cluster_label, 'NMI cluster/label')

ARI cluster/label
metric_barplot(metrics, ARI_cluster_label, 'ARI cluster/label')

Label ASW
metric_barplot(metrics, ASW_label, 'Label ASW')

Isolated label F1
metric_barplot(metrics, isolated_label_F1, 'Isolated label F1')

Isolated label silhouette
metric_barplot(metrics, isolated_label_silhouette, 'Isolated label silhouette')

Graph cLISI
metric_barplot(metrics, cLISI, 'Graph cLISI')

HVG conservation
metric_barplot(metrics, HVG_overlap, 'HVG conservation')

Cell cycle conservation
metric_barplot(metrics, cell_cycle, 'Cell cycle conservation')

Trajectory conservation
metric_barplot(metrics, trajectory, 'Trajectory conservation')

UMAPs
full_src <- list()
for (feature in levels(metrics$features)) {
full_src <- c(
full_src,
paste("##", feature, "{.unnumbered .tabset .tabset-pills .tabset-fade}"),
""
)
for (scale in levels(metrics$scaling)) {
full_src <- c(
full_src,
paste("###", scale, "{.unnumbered .tabset .tabset-pills}"), ""
)
metrics_sel <- filter(metrics, features == feature, scaling == scale)
src_list <- map2_chr(
metrics_sel$method, metrics_sel$output,
function(.method, .output) {
batch_path <- here(
"data", params$dataset,
tolower(scale),
if_else(feature == "Full", "full_feature", "hvg"),
paste(
labels$methods[.method],
case_when(
.output == "Features" ~ "full",
.output == "Embedding" ~ "embed",
.output == "Graph" ~ "knn"
),
"batch.png", sep = "_"
)
)
labels_path <- str_replace(batch_path, "batch", "labels")
src <- c(
"#### <<.method>> - <<.output>> {.tabset .unnumbered}",
"",
"##### Batch {.unnumbered}",
"```{r umap-<<feature>>-<<scale>>-<<.method>>-<<.output>>-batch}",
"knitr::include_graphics('<<batch_path>>')",
"```",
"",
"##### Labels {.unnumbered}",
"```{r umap-<<feature>>-<<scale>>-<<.method>>-<<.output>>-labels}",
"knitr::include_graphics('<<labels_path>>')",
"```",
""
)
knitr::knit_expand(text = src, delim = c("<<", ">>"))
})
full_src <- c(full_src, src_list)
}
}
out <- knitr::knit_child(text = unlist(full_src), options = list(cache = FALSE))
Full
Scaled
MNN - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/mnn_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/mnn_full_labels.png')

Scanorama - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/scanorama_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/scanorama_embed_labels.png')

Scanorama - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/scanorama_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/scanorama_full_labels.png')

Seurat v3 - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/seurat_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/seurat_full_labels.png')

Harmony - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/harmony_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/harmony_embed_labels.png')

BBKNN - Graph
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/bbknn_knn_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/bbknn_knn_labels.png')

ComBat - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/combat_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/combat_full_labels.png')

FastMNN - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/fastmnn_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/fastmnn_embed_labels.png')

FastMNN - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/fastmnn_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/full_feature/fastmnn_full_labels.png')

Unscaled
MNN - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/mnn_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/mnn_full_labels.png')

Scanorama - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/scanorama_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/scanorama_embed_labels.png')

Scanorama - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/scanorama_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/scanorama_full_labels.png')

Seurat v3 - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/seurat_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/seurat_full_labels.png')

Harmony - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/harmony_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/harmony_embed_labels.png')

BBKNN - Graph
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/bbknn_knn_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/bbknn_knn_labels.png')

scVI - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/scvi_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/scvi_embed_labels.png')

ComBat - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/combat_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/combat_full_labels.png')

LIGER - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/liger_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/liger_embed_labels.png')

scANVI - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/scanvi_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/scanvi_embed_labels.png')

FastMNN - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/fastmnn_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/fastmnn_embed_labels.png')

FastMNN - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/fastmnn_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/fastmnn_full_labels.png')

Unintegrated - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/unintegrated_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/full_feature/unintegrated_full_labels.png')

HVG
Scaled
MNN - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/mnn_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/mnn_full_labels.png')

Scanorama - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/scanorama_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/scanorama_embed_labels.png')

Scanorama - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/scanorama_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/scanorama_full_labels.png')

Seurat v3 - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/seurat_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/seurat_full_labels.png')

Harmony - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/harmony_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/harmony_embed_labels.png')

BBKNN - Graph
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/bbknn_knn_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/bbknn_knn_labels.png')

ComBat - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/combat_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/combat_full_labels.png')

FastMNN - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/fastmnn_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/fastmnn_embed_labels.png')

FastMNN - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/fastmnn_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/scaled/hvg/fastmnn_full_labels.png')

Unscaled
MNN - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/mnn_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/mnn_full_labels.png')

Scanorama - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/scanorama_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/scanorama_embed_labels.png')

Scanorama - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/scanorama_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/scanorama_full_labels.png')

Seurat v3 - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/seurat_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/seurat_full_labels.png')

Harmony - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/harmony_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/harmony_embed_labels.png')

BBKNN - Graph
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/bbknn_knn_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/bbknn_knn_labels.png')

scVI - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/scvi_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/scvi_embed_labels.png')

ComBat - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/combat_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/combat_full_labels.png')

LIGER - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/liger_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/liger_embed_labels.png')

scANVI - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/scanvi_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/scanvi_embed_labels.png')

FastMNN - Embedding
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/fastmnn_embed_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/fastmnn_embed_labels.png')

FastMNN - Features
Batch
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/fastmnn_full_batch.png')

Labels
knitr::include_graphics('/Users/luke.zappia/Documents/Projects/scIB-results/data/mini_sim/unscaled/hvg/fastmnn_full_labels.png')
